<tool id="morphological_operations" name="Apply a morphological operation" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0">
    <description>with SciPy</description>
    <macros>
        <import>creators.xml</import>
        <import>tests.xml</import>
        <token name="@TOOL_VERSION@">1.12.0</token>
        <token name="@VERSION_SUFFIX@">1</token>
    </macros>
    <creator>
        <expand macro="creators/bmcv"/>
    </creator>
    <edam_operations>
        <edam_operation>operation_3443</edam_operation>
    </edam_operations>
    <xrefs>
        <xref type="biii">scipy</xref>
    </xrefs>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">scipy</requirement>
        <requirement type="package" version="0.22.0">scikit-image</requirement>
        <requirement type="package" version="0.1">giatools</requirement>
    </requirements>
    <command><![CDATA[
    
    ## Inputs
    
    python '$__tool_directory__/morphological_operations.py' '$image'
    --operation $operation
    --selem-shape $selem_shape
    --selem-size $selem_size
    
    ## Outputs
    
    ./result.tiff
    
    ]]>
    </command>
    <inputs>
        <param name="image" type="data" format="png,tiff" label="Input image" />
        <param label="Morphological operation" argument="--operation" type="select">
            <option value="erosion" selected="True">Erosion</option>
            <option value="dilation">Dilation</option>
            <option value="opening">Opening</option>
            <option value="closing">Closing</option>
            <option value="fill_holes">Fill holes</option>
        </param>
        <param label="Structuring element" argument="--selem-shape" type="select">
            <option value="disk" selected="True">Disk</option>
            <option value="square">Square</option>
        </param>
        <param label="Structuring element size" argument="--selem-size" type="integer" min="1" max="256" value="1" help="The radius of the disk, or the width of the square, in pixels." />
    </inputs>
    <outputs>
       <data format="tiff" name="result" from_work_dir="result.tiff" />
    </outputs>
    <tests>
        <!-- Test binary operations (input images with two distinct values) -->
        <test>
            <param name="image" value="input1.tiff" />
            <param name="operation" value="erosion" />
            <param name="selem_shape" value="disk" />
            <param name="selem_size" value="1" />
            <expand macro="tests/binary_image_diff" name="result" value="output1_erosion.tiff" ftype="tiff"/>
        </test>
        <test>
            <param name="image" value="input1.tiff" />
            <param name="operation" value="dilation" />
            <param name="selem_shape" value="disk" />
            <param name="selem_size" value="2" />
            <expand macro="tests/binary_image_diff" name="result" value="output1_dilation.tiff" ftype="tiff"/>
        </test>
        <test>
            <param name="image" value="input1.tiff" />
            <param name="operation" value="opening" />
            <param name="selem_shape" value="square" />
            <param name="selem_size" value="1" />
            <expand macro="tests/binary_image_diff" name="result" value="output1_opening.tiff" ftype="tiff"/>
        </test>
        <test>
            <param name="image" value="input1.tiff" />
            <param name="operation" value="closing" />
            <param name="selem_shape" value="square" />
            <param name="selem_size" value="2" />
            <expand macro="tests/binary_image_diff" name="result" value="output1_closing.tiff" ftype="tiff"/>
        </test>
        <!-- Test intensity-based operations (more than two distinct values) -->
        <test>
            <param name="image" value="input3.png" />
            <param name="operation" value="erosion" />
            <param name="selem_shape" value="disk" />
            <param name="selem_size" value="1" />
            <expand macro="tests/intensity_image_diff" name="result" value="output3_erosion.tiff" ftype="tiff"/>
        </test>
        <test>
            <param name="image" value="input3.png" />
            <param name="operation" value="dilation" />
            <param name="selem_shape" value="disk" />
            <param name="selem_size" value="2" />
            <expand macro="tests/intensity_image_diff" name="result" value="output3_dilation.tiff" ftype="tiff"/>
        </test>
        <test>
            <param name="image" value="input3.png" />
            <param name="operation" value="opening" />
            <param name="selem_shape" value="square" />
            <param name="selem_size" value="1" />
            <expand macro="tests/intensity_image_diff" name="result" value="output3_opening.tiff" ftype="tiff"/>
        </test>
        <test>
            <param name="image" value="input3.png" />
            <param name="operation" value="closing" />
            <param name="selem_shape" value="square" />
            <param name="selem_size" value="2" />
            <expand macro="tests/intensity_image_diff" name="result" value="output3_closing.tiff" ftype="tiff"/>
        </test>
        <!-- Test multi-channel image (with two distinct values per channel) -->
        <test>
            <param name="image" value="input2.png" />
            <param name="operation" value="fill_holes" />
            <param name="selem_shape" value="disk" />
            <param name="selem_size" value="1" />
            <expand macro="tests/intensity_image_diff" name="result" value="output2_fill_holes.tiff" ftype="tiff"/>
        </test>
    </tests>
    <help>

        **Applies a morphological operation to a 2-D image.**

        For multi-channel images, the operation is applied to each channel separately.

        The following operations are supported:

        - **Erosion:** Shrink bright areas.
        - **Dilation:** Grow bright areas.
        - **Opening:** Erosion followed by Dilation. Erases tiny bright spots.
        - **Closing:** Dilation followed by Erosion. Erases tiny dark holes.
        - **Fill holes:** Fills the holes (dark areas) in binary images.

    </help>
    <citations>
        <citation type="doi">10.1038/s41592-019-0686-2</citation>
    </citations>
</tool>